Yesterday I officially ended my 23rd and final year of schooling. I am graduating with a doctoral degree in Structural and Computational Biology and Molecular Biophysics. For the last 7 years I have worked on attaining that degree, and finally yesterday this part of my journey was completed. Since this research has consumed my life, I thought a beautiful and fulfilling conclusion to this would be to share with you how MY scientific studies parallel a life of faith. I promise to try my very best to not get lost in the scientific details or rant about it as I could for hours on end. Let’s go.
So the general method of research that I utilize is called Molecular Dynamics (MD) Simulations. The general idea behind MD is that you use a computer to make simulations of very tiny molecules and how they move because experimental techniques are not yet able to visualize movement of such tiny things.
What? How does that work?
A bunch of people much smarter than me created a computer program that replicates as many of nature’s forces as possible. (van der Waals, electrostatics, etc) Then I add a bunch of molecules into a box that are similar to the real life system. (waters, ions, my protein I’m studying) Then I basically click start and it creates a simulation of how that protein would naturally act in that system that I created. THEN the real work starts; I analyze the data from the simulations.
For the last 6 of my 7 years I’ve been running a bunch of different simulations on one specific protein in one of these boxes. This protein is LacI.
Oooo! Pretty! So what does this thing do? In humans our favored energy source is glucose. This is true for lots of creatures, but in many bacteria when glucose isn’t available it takes in lactose and needs some way to digest it. So the lac genes create proteins/enzymes that are able to digest lactose. BUT it would be SUCH a waste to create these enzymes when there is no lactose to digest. So there has to be some way to regulate the creation of these enzymes. Enter stage right the glorious “lac repressor protein” aka “LacI.” When there is no lactose anywhere nearby, it binds to a specific sequence of DNA and says STOP RIGHT THERE! DON’T DO IT! DON’T YOU DARE MAKE THOSE ENZYMES!
Cool. All of that has been known since the 1950s. So what am I doing that is new and innovative? All of those studies of it were with experimental techniques. Like I said before, those can’t look at the movements of tiny proteins. Instead it can only get individual images of them when it’s stuck in a specific crystal structure. So the secret I didn’t tell you about this nifty protein is that a tiny little segment called the hinge helix is a beautiful pretty helix when it is bound to that specific segment of DNA and it’s putting on the brakes of creation, but when it is on any other DNA segment or if it’s out in the solution it loses that shape and becomes flexible like a piece of cooked spaghetti. My studies were looking at what shape that spaghetti prefers and the energy that causes it to look like that.
After a few years of study when I started getting some results, my mind got blown, first by the scientific implications of my findings, second by the correlation of those findings to faith. The results said the difference in energy between the perfect helix and the disordered preferred state was 40-60 kcal/mol!!! For those of you non-scientists out there, a change/reaction will only ever really happen on it’s own up to like 5-10 kcal/mol. That means this is WAY bigger than that. So this protein will NEVER EVER EVER go up to that pretty perfect helix shape on its own. It’ll always stay squiggly spaghetti. When the protein is in an environment that’s SIMILAR to that near the segment of DNA, that difference changes to only 10 kcal/mol. In this environment it takes very little (but still some extra energy) to get it to that perfect helix. Great!
You and I are this protein.
Think about it.
When we try to do things on our own, we will fail. We stay in our imperfect form. First due to original sin, then due to any other sin after that. If God is not at all a part of our life, it is impossible for us to attain this perfection that we desire. (whether we know we want it or not)
If we are living a good life but don’t have God, we are like the protein in the second environment. We’re so close. It is much easier to transition from this state to our most perfect form, but there is still a lot of work to get there. We still need some outside power to come push us over that hump. We can’t do it on our own.
So, something I didn’t talk about yet is that in order to get to the CORRECT DNA segment, the protein binds to the wrong DNA and slides along it until it finds the correct stuff. This is the life of the faithful while here on earth. We are searching for God. We are on the right path, but we are still in our brokenness. We are still in our earthly form. BUT at this point you ARE bound to something greater than yourself and you are heading towards that perfection in heaven.
Then, finally, the goal for all of us is to be fully united with God in heaven. It is only through the love and mercy of God that we will ever reach that perfect form. We must be in full communion with God as the protein must be bound to the correct DNA sequence.
This is even a more perfect analogy because the terms for the “perfect form” and the “spaghetti form” are “ordered” and “disordered.” The terminology that many people use for our desires and our actions are to say they are “ordered” or “disordered.” We are called to perfectly ordered love of God and neighbor, but often our desires become disordered and we give that love in imperfect ways. I hear that saying a lot. When we order our desires and our lives towards the perfect God then our lives become more ordered. Even in the chaos we can find peace.
Now there is a lot more to this protein than this shape change and the energy behind it, but that’s not what I studied. I studied this little piece of the puzzle. I am so happy to say that I have transitioned between these states throughout my last 7 years. I’ve grown in my scientific knowledge, but I’ve also grown in my knowledge of the Church and my personal faith life. Sometimes these 7 years have been horribly difficult, sometimes it’s brought me unimaginable joy. It is undeniable that I have grown and that I am better now than I was before.